I had this same issue. I found somewhere (can not find now) the instructions to fix it.

It has to do with the service book.

If I remember, you go to service books under advanced options. Delete the Desktop CMME service book. Them as soon as you do that undlete it. Then have your IT guy send the service book to your phone. (This step may not be necessary but I did it anyway)

It will take about 5 minutes then your phone should start to reconcile.

I have done this to 3 8100's now and it worked on all of them.

CMME is for calendar and will address issues with calendar sync. For your reconcile issue, delete the desktop sync and repush. This should bring back the mail store settings to where you can see all 3 settings in the email reconciliation. Usually a reboot will fix this (sometimes). If not, delete the desktop sync and have your BB Admin repush the service book. You will see the Desktop Sync re-populate in the service books and you should then be able to see all settings again...